This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Mass spectrometry is a method of choice for quantifying low abundance proteins and peptides and it has been applied to many areas of biology. We are developing a range of computational methods for protein and peptide quantification, including methods for finding and integrating peaks of interest, and detecting interference to obtain a robust measure of the amount of material present in the samples. A paper describing this work has been published: Zhang G, Ueberheide BM, Waldemarson S, Myung S, Molloy K, Eriksson J, Chait BT, Neubert TA, Feny[unreadable] D Protein quantitation using mass spectrometry Methods Mol Biol. 2010;673:211-22